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FFPred 3: feature-based function prediction for all Gene Ontology domains

Domenico Cozzetto, Federico Minneci, Hannah Currant, David T. Jones
2016 Scientific Reports  
Predicting protein function has been a major goal of bioinformatics for several decades, and it has gained fresh momentum thanks to recent community-wide blind tests aimed at benchmarking available tools on a genomic scale. Sequence-based predictors, especially those performing homology-based transfers, remain the most popular but increasing understanding of their limitations has stimulated the development of complementary approaches, which mostly exploit machine learning. Here we present
more » ... 3, which is intended for assigning Gene Ontology terms to human protein chains, when homology with characterized proteins can provide little aid. Predictions are made by scanning the input sequences against an array of Support Vector Machines (SVMs), each examining the relationship between protein function and biophysical attributes describing secondary structure, transmembrane helices, intrinsically disordered regions, signal peptides and other motifs. This update features a larger SVM library that extends its coverage to the cellular component sub-ontology for the first time, prompted by the establishment of a dedicated evaluation category within the Critical Assessment of Functional Annotation. The effectiveness of this approach is demonstrated through benchmarking experiments, and its usefulness is illustrated by analysing the potential functional consequences of alternative splicing in human and their relationship to patterns of biological features.
doi:10.1038/srep31865 pmid:27561554 pmcid:PMC4999993 fatcat:axqwxm4d2fbixjuh7c3xi6eyky

BayesPiles

Athanasios Vogogias, Jessie Kennedy, Daniel Archambault, Benjamin Bach, V. Anne Smith, Hannah Currant
2018 ACM Transactions on Intelligent Systems and Technology  
We address the problem of exploring, combining and comparing large collections of scored, directed networks for understanding inferred Bayesian networks used in biology. In this eld, heuristic algorithms explore the space of possible network solutions, sampling this space based on algorithm parameters and a network score that encodes the statistical t to the data. e goal of the analyst is to guide the heuristic search and decide how to determine a nal consensus network structure, usually by
more » ... cting the top-scoring network or constructing the consensus network from a collection of high-scoring networks. BayesPiles, our visualisation tool, helps with understanding the structure of the solution space and supporting the construction of a nal consensus network that is representative of the underlying dataset. BayesPiles builds upon and extends MultiPiles to meet our domain requirements. We developed BayesPiles in conjunction with computational biologists who have used this tool on datasets used in their research. e biologists found our solution provides them with new insights and helps them achieve results that are representative of the underlying data.
doi:10.1145/3230623 fatcat:vwu2n53jtze5fiyk7a4pkgcqwe

MLCut: Exploring Multi-Level Cuts in Dendrograms for Biological Data [article]

Athanasios Vogogias, Jessie Kennedy, Daniel Archambault, V. Anne Smith, Hannah Currant
2016 Computer Graphics and Visual Computing (CGVC)  
Choosing a single similarity threshold for cutting dendrograms is not sufficient for performing hierarchical clustering analysis of heterogeneous data sets. In addition, alternative automated or semi-automated methods that cut dendrograms in multiple levels make assumptions about the data in hand. In an attempt to help the user to find patterns in the data and resolve ambiguities in cluster assignments, we developed MLCut: a tool that provides visual support for exploring dendrograms of
more » ... neous data sets in different levels of detail. The interactive exploration of the dendrogram is coordinated with a representation of the original data, shown as parallel coordinates. The tool supports three analysis steps. Firstly, a single-height similarity threshold can be applied using a dynamic slider to identify the main clusters. Secondly, a distinctiveness threshold can be applied using a second dynamic slider to identify "weak-edges" that indicate heterogeneity within clusters. Thirdly, the user can drill-down to further explore the dendrogram structure - always in relation to the original data - and cut the branches of the tree at multiple levels. Interactive drill-down is supported using mouse events such as hovering, pointing and clicking on elements of the dendrogram. Two prototypes of this tool have been developed in collaboration with a group of biologists for analysing their own data sets. We found that enabling the users to cut the tree at multiple levels, while viewing the effect in the original data, is a promising method for clustering which could lead to scientific discoveries.
doi:10.2312/cgvc.20161288 dblp:conf/tpcg/VogogiasKASC16 fatcat:abhkq53dnjfdnnigfrdattly7a

Comparison of Associations with Different Macular Inner Retinal Thickness Parameters in a Large Cohort: The UK Biobank

Anthony P. Khawaja, Sharon Chua, Pirro G. Hysi, Stelios Georgoulas, Hannah Currant, Tomas W. Fitzgerald, Ewan Birney, Fang Ko, Qi Yang, Charles Reisman, David F. Garway-Heath, Chris J. Hammond (+4 others)
2019 Ophthalmology (Rochester, Minn.)  
To describe and compare associations with macular retinal nerve fiber layer (mRNFL), ganglion cell complex (GCC), and ganglion cell-inner plexiform layer (GCIPL) thicknesses in a large cohort. Cross-sectional study. We included 42 044 participants in the UK Biobank. The mean age was 56 years. Spectral-domain OCT macular images were segmented and analyzed. Corneal-compensated intraocular pressure (IOPcc) was measured with the Ocular Response Analyzer (Reichert, Corp., Buffalo, NY). Multivariable
more » ... linear regression was used to examine associations with mean mRNFL, GCC, and GCIPL thicknesses. Factors examined were age, sex, ethnicity, height, body mass index (BMI), smoking status, alcohol intake, Townsend deprivation index, education level, diabetes status, spherical equivalent, and IOPcc. Thicknesses of mRNFL, GCC, and GCIPL. We identified several novel independent associations with thinner inner retinal thickness. Thinner inner retina was associated with alcohol intake (most significant for GCIPL: -0.46 μm for daily or almost daily intake compared with special occasion only or never [95% confidence interval (CI), 0.61-0.30]; P = 1.1×10-8), greater social deprivation (most significant for GCIPL: -0.28 μm for most deprived quartile compared with least deprived quartile [95% CI, -0.42 to -0.14]; P = 6.6×10-5), lower educational attainment (most significant for mRNFL: -0.36 μm for less than O level compared with degree level [95% CI, -0.45 to 0.26]; P = 2.3×10-14), and nonwhite ethnicity (most significant for mRNFL comparing blacks with whites: -1.65 μm [95% CI, -1.86 to -1.43]; P = 2.4×10-50). Corneal-compensated intraocular pressure was associated most significantly with GCIPL (-0.04 μm/mmHg [95% CI, -0.05 to -0.03]; P = 4.0×10-10) and was not associated significantly with mRNFL (0.00 μm/mmHg [95% CI, -0.01 to 0.01]; P = 0.77). The variables examined explained a greater proportion of the variance of GCIPL (11%) than GCC (6%) or mRNFL (7%). The novel associations we identified may be important to consider when using inner retinal parameters as a diagnostic tool. Associations generally were strongest with GCIPL, particularly for IOP. This suggests that GCIPL may be the superior inner retinal biomarker for macular pathophysiologic processes and especially for glaucoma.
doi:10.1016/j.ophtha.2019.08.015 pmid:31585827 fatcat:kin7ooorszc23ldwsbyxrjyyum

Genetic variation affects morphological retinal phenotypes extracted from UK Biobank Optical Coherence Tomography images [article]

Hannah Currant, Pirro Hysi, Tomas W Fitzgerald, Puya Gharahkhani, Pieter W M Bonnemaijer, Denize Atan, Tin Aung, Jason Charng, Hélène Choquet, Jamie Craig, Alex W Hewitt, Peng T Khaw (+20 others)
2020 medRxiv   pre-print
Optical Coherence Tomography (OCT) enables non-invasive imaging of the retina and is often used to diagnose and manage multiple ophthalmic diseases including glaucoma. We present the first large-scale quantitative genome-wide association study of inner retinal morphology using phenotypes derived from OCT images of 31,434 UK Biobank participants. We identify 46 loci associated with thickness of the retinal nerve fibre layer or ganglion cell inner plexiform layer. Only one of these loci has
more » ... usly been associated with glaucoma, and Mendelian randomisation confirms that inner retinal thickness, despite being a valid biomarker for the disease, is not on the same genetic causal pathway as glaucoma. Image analysis methods were used to extract overall retinal thickness at the fovea, representative of hypoplasia, with which three out of the 46 SNPs were associated. These SNPs have been previously linked with pigmentation, confirmed by their association with hair colour in the UK Biobank dataset. We additionally associate these three loci with visual acuity. In contrast to the already known Mendelian causes of severe foveal hypoplasia, our results suggest a previously unknown spectrum of foveal hypoplasia in the population, in part genetically determined, that has consequences on visual function.
doi:10.1101/2020.07.20.20157180 fatcat:rfl5ffragbgb5edajhhxq6hsle

Page 516 of American Spirit Vol. 64, Issue 8 [page]

1930 American Spirit  
Bailey, John Currant, Elizabeth Rosier, John Hull, Narcisus Dorrow, Robert Jones, Barbara Richardson, Wm. Baker, Christena . Sine, Jacob Piles, Hannah. .  ...  Jones, Christina Carney, Michael Michael, Henry Lantz, John Chipps, Hannah Patterson, Philip Ewell, Thomas Currant, Enoch Hull, Jacob Jones, David. . Baker, Wm.. .  ... 

Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images

Hannah Currant, Pirro Hysi, Tomas W. Fitzgerald, Puya Gharahkhani, Pieter W. M. Bonnemaijer, Anne Senabouth, Alex W. Hewitt, Denize Atan, Tin Aung, Jason Charng, Hélène Choquet, Jamie Craig (+25 others)
2021 PLoS Genetics  
Optical Coherence Tomography (OCT) enables non-invasive imaging of the retina and is used to diagnose and manage ophthalmic diseases including glaucoma. We present the first large-scale genome-wide association study of inner retinal morphology using phenotypes derived from OCT images of 31,434 UK Biobank participants. We identify 46 loci associated with thickness of the retinal nerve fibre layer or ganglion cell inner plexiform layer. Only one of these loci has been associated with glaucoma,
more » ... despite its clear role as a biomarker for the disease, Mendelian randomisation does not support inner retinal thickness being on the same genetic causal pathway as glaucoma. We extracted overall retinal thickness at the fovea, representative of foveal hypoplasia, with which three of the 46 SNPs were associated. We additionally associate these three loci with visual acuity. In contrast to the Mendelian causes of severe foveal hypoplasia, our results suggest a spectrum of foveal hypoplasia, in part genetically determined, with consequences on visual function.
doi:10.1371/journal.pgen.1009497 pmid:33979322 pmcid:PMC8143408 fatcat:opm7p2h335hlplq765h4ahjwuq

Page 14 of Argosy Vol. 30, Issue [page]

1880 Argosy  
On this evening, quite late, Hannah Tilney, the gardener’s wife at the lodge, came up to the Hall. It was past nine o’clock. Her errand was to ask Mrs. Stone for a small pot of black currant jelly.  ...  ‘He has got one of them sore throats come on,” said Hannah.  ... 

Page 258 of The New England Historical and Genealogical Register Vol. 14, Issue 3 [page]

1860 The New England Historical and Genealogical Register  
be to be had, if not then te pay in currant pay at money price as indifferent men shall judge, if you cannot agree amongst yourselves, & my will is yt y* said James Tucker doing thus shall have up his  ...  Only if I dye before James Tucker pay me £10 in money of New 2 then my will is that he, the said Tucker, shall pay to Isaac two oldest daut Ruth & Mary £5 apeice in currant money of New Eng. land, if it  ... 

Page 242 of American Spirit Vol. 63, Issue 4 [page]

1929 American Spirit  
Hall, William Currant, James Royce, Isaac Mellett, Jesse Miller, Thomas (Dec’d.)  ...  Exline, Solomon Smith, Jane Durant, Nathan Morgan, Mary M Parrish, Jesse Bright, Elizabeth Hurley, William Newbrough, Hannah White, Isaac Collins, Sarah Allen, George D.  ... 

Page 614 of American Spirit Vol. 63, Issue 10 [page]

1929 American Spirit  
Tabler, Phebe Wolfe, John Clark, Jane Kennedy, Peter Dunlap, Mary Emmerson, Joseph Collins, Hannah McCaslin, Maxwell Kirk, Eliza... .. Henderson, Mathew Fetty, Mary. .  ...  Hannan, Martha Martin, Henson Currant, Jane. Thorp, James Moaham, Arah. Moreland, Eli Tricket, Mary Johnson, Samuel Jolliffe, Mary Scrannage, Wm.  ... 

Page 903 of New England Farmer; A Monthly Journal Vol. 1, Issue 8 [page]

1867 New England Farmer; A Monthly Journal  
HANNAH. ABOUT CURRANTS. Currants Preserved.  ...  Currant Wine.  ... 

Page 577 of The New Monthly Magazine Vol. 4, Issue 23 [page]

1873 The New Monthly Magazine  
Hannah expressed the feelings of the country in general when she said to Lucy, who was standing before the press “in the storeroom, giving out currants and raisins, and, consequentiy, could not escape  ...  ‘Miss Elton will make him quite happy, Hannah, and he is very fond of her.’’ ‘* Well, well, dear!  ... 

Page 356 of The Cornhill Magazine Vol. 52, Issue 309 [page]

1922 The Cornhill Magazine  
I have seen a pair of net curtains in the sere and yellow protecting red currant bushes from the ravages of birds in the old garden.  ...  356 AUNT HANNAR’S AUNT HANNAH was not a cannibal ; further examination discloses—‘ Missionary box 1s. 2d.,’ which clears the matter up.  ... 

Page 168 of The New England Historical and Genealogical Register Vol. 14, Issue 2 [page]

1860 The New England Historical and Genealogical Register  
On ‘the 14th Currant dyed here Mrs Mary Godferry in the 82d year of her Age, being the first English Child born in this Town.”— Boston News-Letter, April 16 to 23, 1716. * Minor Diary.  ...  Robert Burdick), Daniel, and Hannah. James m. Sarah Babcock, dau. of James, Jr. David m. Elizabeth Babcock, dau. of James, Jr. Isreal m. Jane, dau. of James Babcock, Jr., and had Isreal b.  ... 
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